The genome sequence of the particolored bat, Vespertilio murinus Linnaeus, 1758

We present a genome assembly from an individual male Vespertilio murinus (the particolored bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence is 1,925.6 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.96 kilobases in length.


Background
The Parti-coloured bat (Vespertilio murinus) is a medium-sized bat, characterised by its long fur on the back that is unmistakably bicoloured: a dark brown base and silvery white tips (Figure 1).Until the 20th century, the species has been confounded in literature with the Greater mouse-eared bat (Myotis myotis, Borkhausen 1797) that originally was named Vespertilio murinus by Borkhausen, the reason for which some authors used the name 'Vespertilio discolor' for the Parti-coloured bat (Rydell & Baagøe, 1994).
The species is listed by the IUCN Red list as "Least Concern" globally with a stable population trend (Coroiu, 2016), although it is not considered common in large parts of its range.It has a wide distribution in the northern Palaearctic, from France and Britain in the west, through central, northern and eastern Europe and Siberia to the Pacific coast.The southern limit of its range passes through the Balkans, central Asia and China (Coroiu, 2016).In parts of its range, it is known to migrate seasonally over long distances up to over 800 kilometres (Masing, 1989) and single movements as far as 1787 kilometres are known (Markovets et al., 2004), and so are offshore detections (Brabant et al., 2020).
With a litter size of two, or rarely three, offspring that is typical for migratory species, the females have two pairs of functional teats, which is a unique feature of this species and distinguishes it from all other European bat species (Safi, 2006).Overall, there is very little sexual dimorphism.The maximum life span has been reported to be 12 years, based on one ringed individual (Červený & Bürger, 1989).
In summer, the species is known to roost mainly in buildings, exceptionally in trees.Remarkably, winter roosts are not known, apart from anecdotal findings of individuals (Safi, 2006).Females prefer to forage over large open waters, while males also hunt along rivers, over large agricultural or urban areas.Its preference for open areas makes the species particularly vulnerable for wind turbines.
The genome of the particolored bat, Vespertilio murinus, was sequenced as part of the Darwin Tree of Life Project (DToL) project, the Bat1K Project and the Vertebrate Genomes Project (VGP).Here we present a chromosomally complete genome sequence for Vespertilio murinus, based on one male specimen from Ostend, Belgium.

Genome sequence report
The genome was sequenced from a male Vespertilio murinus collected from Ostend, Belgium.A total of 44-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 49 missing joins or mis-joins and removed 4 haplotypic duplications, reducing the scaffold number by 11.88%.
The final assembly has a total length of 1,925.6Mb in 177 sequence scaffolds with a scaffold N50 of 186.3 Mb (Table 1).The snail plot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (97.66%) of the assembly sequence was assigned to 20 chromosomal-level scaffolds, representing 18 autosomes and the X and Y sex chromosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.

Sample acquisition and nucleic acid extraction
The specimen collected for this research, an adult male Vespertilio murinus (specimen ID SAN00002659, ToLID mVesMur1), was suffering upper arm (humerus) fracture, with a nearby wind turbine as a plausible cause.The animal was collected on 2022-09-08 by the Ostend Wildlife Rehab centre, who contacted the author (Bob Vandendriessche) for advice.MitoFinder (Allio et al., 2020) or MITOS (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
The sanger-tol/blobtoolkit pipeline is a Nextflow port of the previous Snakemake Blobtoolkit pipeline (Challis et al., 2020).It aligns the PacBio reads with SAMtools and mini-map2 (Li, 2018) and generates coverage tracks for regions of fixed size.In parallel, it queries the GoaT database (Challis et al., 2023) to identify all matching BUSCO lineages to run BUSCO (Manni et al., 2021).For the three domain-level BUSCO lineage, the pipeline aligns the BUSCO genes to the Uniprot Reference Proteomes database (Bateman et al., 2023) with DIAMOND (Buchfink et al., 2021) blastp.The genome is also split into chunks according to the density of the BUSCO genes from the closest taxonomically lineage, and each   chunk is aligned to the Uniprot Reference Proteomes database with DIAMOND blastx.Genome sequences that have no hit are then chunked with seqtk and aligned to the NT database with blastn (Altschul et al., 1990).All those outputs are combined with the blobtools suite into a blobdir for visualisation.
All three pipelines were developed using the nf-core tooling (Ewels et al., 2020), use MultiQC (Ewels et al., 2016), and make extensive use of the Conda package manager, the Bioconda initiative (Grüning et al., 2018)  Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use.The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material

Wenhua Yu
Guangzhou University, Guangzhou, China This manuscript reports the genomic information of Vespertilio murinus, which can provide important foundational data for subsequent comparative genomics and genomic analyses.The analysis methods used in the paper are reasonable, the structure is complete, and the data is detailed.I have a few minor suggestions for the authors to consider and revise in order to further enhance the quality of the paper.
In Figure 1, is the grids a spider web?It is suggested to clarify this in the figure legend because it is odd. 1.
It is recommended to supplement an explanation of the tissue from which the genome was derived.

2.
Please check the data in the figures, tables, and text for consistency; there is a discrepancy in the number of scaffolds.

3.
I personally suggest that the authors supplement the annotation work, as this is crucial for future research.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes 7. Why no annotation information was contained in this study?I think a high-quality annotated genome will be a valuable resource for following genomic analyses across species, for population genomics, and for future evolutionary investigations, which could improve the significance of genome sequencing.
Is the rationale for creating the dataset(s) clearly described?Yes Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Partly
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: animal behavior; animal ecology I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 1 .
Figure 1.A male Vespertilio murinus resting on the outside of a large building at the seafront in Blankenberge, Belgium, 13 Sept. 2023.Along the North Sea coast, this behaviour has been observed frequently in this species -as it is in Pipistrellus nathusii -during migration.(Image © Bob Vandendriessche).

Figure 2 .
Figure 2. Genome assembly of Vespertilio murinus, mVesMur1.1:metrics.The BlobToolKit snail plot shows N50 metrics and BUSCO gene completeness.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 1,925,577,803 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (219,009,580 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (186,292,382 and 49,547,305 bp), respectively.The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude.The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot.A summary of complete, fragmented, duplicated and missing BUSCO genes in the laurasiatheria_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Vespertilio_murinus/dataset/GCA_963924515.1/snail.

Figure 3 .
Figure 3. Genome assembly of Vespertilio murinus, mVesMur1.1:BlobToolKit GC-coverage plot.Sequences are coloured by phylum.Circles are sized in proportion to sequence length.Histograms show the distribution of sequence length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Vespertilio_murinus/dataset/GCA_963924515.1/blob.

Figure 4 .
Figure 4. Genome assembly of Vespertilio murinus mVesMur1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all sequences.Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Vespertilio_murinus/dataset/GCA_963924515.1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Vespertilio murinus mVesMur1.1:Hi-C contact map of the mVesMur1.1 assembly, visualised using HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=MQFBPCWcQBGnl_BQz6w8Fw.

Table 1 . Genome data for Vespertilio murinus, mVesMur1.1. Project accession data
(Narváez-Gómez et al., 2023) are adapted from column VGP-2020 of "Table1: Proposed standards and metrics for defining genome assembly quality" fromRhie et al. (2021).tionat the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up.In sample preparation, the mVesMur1 sample was weighed and dissected on dry ice(Jay  et al., 2023).For sample homogenisation, tissue was cryogenically disrupted using the Covaris cryoPREP ® Automated Dry Pulverizer(Narváez-Gómez et al., 2023).ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA.The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer, Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit.Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

Darwin Tree of Life Project Sampling Code of Practice', which
can be found in full on the Darwin Tree of Life website here.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standardsset out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.

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